ITS reference alignment

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peleliu
Posts: 52
Joined: Sun Jul 25, 2010 6:37 am

ITS reference alignment

Post by peleliu » Thu May 10, 2018 8:12 am

Hi,
Is there a good reference alignment for usage with ITS data in align.seqs?
I tried ITSdb.findley.fasta but got an error that the template is not aligned and Mothur aborted.
Any suggestions?
Thanks!

kmitchell
Posts: 495
Joined: Wed Mar 10, 2010 8:19 pm
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Re: ITS reference alignment

Post by kmitchell » Wed May 16, 2018 4:41 am

In general, ITS evolves too quickly to be aligned. If you are working with just a small taxonomic group, you could create you own alignment. But if you are working with all fungi, you can not align ITS/ITS2

peleliu
Posts: 52
Joined: Sun Jul 25, 2010 6:37 am

Re: ITS reference alignment

Post by peleliu » Wed May 16, 2018 8:32 am

OK then, what are the preferred primers (the "16S equivalent") for working with fungi?

kmitchell
Posts: 495
Joined: Wed Mar 10, 2010 8:19 pm
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Re: ITS reference alignment

Post by kmitchell » Fri May 25, 2018 1:12 pm

sorry, missed your followup. I do use ITS2 even though we can't align it. It gives the best taxonomic resolution that we can get for all fungi. If you are working with specific groups of fungi, you may want to choose a different target.

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